Also, regarding the real ship names in your Commander patrol logs - you need to update your personnel file after the patrol before reviewing the logs. Updating your personnel file is what triggers Commander to flesh out the patrol log with real ship info. If you choose to review your patrol log before udating your personnel file, the log is generated without real ship info.
The other two "rules" mentioned are also a good bet for more trouble-free playing: click the Auto Rollback option in Commander, and don't upgrade your boat/equipment before starting your first patrol.
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